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- EMDB-55123: Structure of 70S ribosome-apramycin complex with tRNAs in classic... -

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Basic information

Entry
Database: EMDB / ID: EMD-55123
TitleStructure of 70S ribosome-apramycin complex with tRNAs in classic state (C)
Map data
Sample
  • Complex: Structure of the 70S ribosome complex with tRNAs in classic state (C)
KeywordsEF-G / robosome / 70S / apramycin / translocation / RIBOSOME / mutation
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.53 Å
AuthorsGhosh Dastidar N / Freyer N / Petrychenko V / Schwarzer AC / Peng BZ / Samatova E / Kothe C / Schmidt M / Peske F / Politi A ...Ghosh Dastidar N / Freyer N / Petrychenko V / Schwarzer AC / Peng BZ / Samatova E / Kothe C / Schmidt M / Peske F / Politi A / Urlaub H / Fischer N / Rodnina MV / Wohlgemuth I
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Leibniz Prize (to M.V.R.) & SFB 860 Germany
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2025
Title: Selective silencing of antibiotic-tethered ribosomes as a resistance mechanism against aminoglycosides.
Authors: Nilanjan Ghosh Dastidar / Nicola S Freyer / Valentyn Petrychenko / Ana C de A P Schwarzer / Bee-Zen Peng / Ekaterina Samatova / Christina Kothe / Marlen Schmidt / Frank Peske / Antonio Z ...Authors: Nilanjan Ghosh Dastidar / Nicola S Freyer / Valentyn Petrychenko / Ana C de A P Schwarzer / Bee-Zen Peng / Ekaterina Samatova / Christina Kothe / Marlen Schmidt / Frank Peske / Antonio Z Politi / Henning Urlaub / Niels Fischer / Marina V Rodnina / Ingo Wohlgemuth /
Abstract: Antibiotic resistance is a growing threat, underscoring the need to understand the underlying mechanisms. Aminoglycosides kill bacteria by disrupting translation fidelity, leading to the synthesis of ...Antibiotic resistance is a growing threat, underscoring the need to understand the underlying mechanisms. Aminoglycosides kill bacteria by disrupting translation fidelity, leading to the synthesis of aberrant proteins. Surprisingly, mutations in fusA, a gene encoding translation elongation factor G (EF-G), frequently confer resistance, even though EF-G neither participates in mRNA decoding nor blocks aminoglycoside binding. Here, we show that EF-G resistance variants selectively slow ribosome movement along mRNA when aminoglycosides are bound. This delay increases the chance that the drug dissociates before misreading occurs. Over several elongation cycles, this selective silencing of drug-bound ribosomes prevents error cluster formation, preserving proteome and membrane integrity. As a result, fusA mutations confer resistance early in treatment by preventing self-promoted aminoglycoside uptake. Translation on drug-free ribosomes remains sufficiently rapid to sustain near-normal bacterial growth. The mechanism of selective silencing of corrupted targets reveals a previously unrecognized antibiotic resistance strategy with potential therapeutic implications.
History
DepositionSep 23, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55123.png

Downloads & links

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Map

FileDownload / File: emd_55123.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesX (Sec.)Y (Row.)Z (Col.)
1.16 Å/pix.
x 288 pix.
= 334.08 Å		1.16 Å/pix.
x 288 pix.
= 334.08 Å		1.16 Å/pix.
x 288 pix.
= 334.08 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
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Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-8.176409 - 22.830100999999999
Average (Standard dev.)-0.000000000000185 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 334.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55123_msk_1.map
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Additional map: #1

Fileemd_55123_additional_1.map
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Half map: #1

Fileemd_55123_half_map_1.map
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Half map: #2

Fileemd_55123_half_map_2.map
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Sample components

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Entire : Structure of the 70S ribosome complex with tRNAs in classic state (C)

EntireName: Structure of the 70S ribosome complex with tRNAs in classic state (C)
Components
  • Complex: Structure of the 70S ribosome complex with tRNAs in classic state (C)

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Supramolecule #1: Structure of the 70S ribosome complex with tRNAs in classic state (C)

SupramoleculeName: Structure of the 70S ribosome complex with tRNAs in classic state (C)
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli K-12 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 50 mM HEPES, 70 mM NH4Cl, 30 mM KCl, 3.5 mM MgCl2, 0.6 mM spermine, 0.4 mM spermidine
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: HOMEMADE PLUNGER / Details: Manual blotting & plunge-freezing.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1753901
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

10906

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 1130316
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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